SCAN-2 Comparison of genomic sequences with Java visualization

webmaster webmaster at softberry.com
Thu Dec 7 05:37:18 EST 2000


SCAN-2 Comparison of genomic sequences with Java visualization
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SCAN-2 is developed to compare 2 orthologous  regions of some genomes (as Human and Mouse, for example) with Java viewer which helps to investigate and visualize similar subregions. Scan-2 uses a new fast sequence comparison algorithm developed in Softberry Inc.

SCAN-2 is available for public usage at: 

http://www.softberry.com/scan.html

Here is an example of alignment fragment:

scan2ex  Mon Dec  4 20:45:15 EST 2000
gi|455025|gb|U01317.1|HUMHBB Human beta globin egion on chomosome 11 vs.  .
[D] Sequence       1, S:        8850, gi|1418273|gb|U60902.1|OCU60902 Otolemu cassicaudatus epsilon-, gamma-, delta-, and beta-globin genes, complete cds, and eta-globin pseudogene
         5         5        11        21        31       522
         ----------(..)tctaatctccCTCTCAACCCtacagtcacc(..)ttaattttgtAA
         attaatagtt(..)tgactatacaCTCTCAACCCagtttccata(..)ttagcttgacAA
         1      1998      2004      2014      2024      2274

       532       542       552       562       572       582
         TATTGATATTATTCCTAGAAAGCTGAGGCCTCAAGATGATAACTTTTATTttctggactt
         TATTGATATTATCAATAGAAGGTTGAGGCCTAAAGGTGATGACTTTTATTcatttattta
      2284      2294      2304      2314      2324      2334

       730       736       746       756       766       776
         (..)atgggaaaacAAGTATGTACTTTTTCTACTAAGCCATTGAAACAGGAATAACAGAA
         (..)-gagaaaagaAAGTATACACTTTACCTACTAAGCCATTGAAGCATGAATAATAAAA
      2469      2474      2484      2494      2504      2514
…………………………………..

Java Viewer of Alignment Results –SCAN2 Program
The viewer has four main panels: 
General View Panel (Top of the viewer window)
Selected Alignment Panel (Middle of the window)
Alignnment Selection Panel (Bottom of the window)
Output Message Panel (one-line panel at the very bottom of the window).

General View Panel

Graphical view of full-length alignment is drawn as two horizontal bars, each representing one sequence. High homology regions are drawn in red, regions of low or no homology - in yellow, and stretches of one sequence opposite to gaps in another sequence are drawn in gray. Pink homology profile is located above an alignment. 
There are two horizontal scroll bars at the bottom of the panel: first one is a regular scroll bar, the second one is for zooming an alignment in and out.
When mouse cursor points to one of the bars, information about the region is displayed  in Output Message panel: homology percentage, length, coordinates of start of the region on first and and second sequence. You can select a region on alignment by pressing left mouse button and dragging. Aligned sequence of selected region will be displayed in Detail View panel.   Marking a region by Shift+Click opens selected sequence in a separate browser window, from where it can be saved or copied to other applications.




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